On Mon, Sep 26, 2011 at 11:22, Dmitry <[email protected]> wrote: > > Could anybody change INB repository address in BioMoby Taverna plug-in please? > The current plug-in points into developers repository and not to a production > one. > I already changed it in BioMoby repository, but unfortunately I have little > knowledge how BioMoby Taverna plug-in is built. > As far as I understand taverna uses it's own build scripts. Does it use > BioMoby (OpenBio) repository? Why the plug-in itself is in Taverna maven > repository and not in BioMoby maven?
Could you detail which repository should be removed, and which should be added? See [1] for the current setting used by Taverna at runtime - and [2][3] for dependencies used at build-time - repositories for building are declared in [4][5] - that is also our mirror [6]. Note that [6] is a (weekly) mirror of [7] due to the repeated instability of the network connection (and future accessibility) of http://biomoby.org/ - done as: #!/bin/bash set -e # exit on error cd /local/www/mygrid/maven/biomoby wget --reject 'index.html*' --no-parent --random-wait --wait 0.1 --no-verbose --tries=3 --retry-connrefused --mirror http://biomoby.org/m2repo/ Please also note that the biomoby activity is depending on a slightly patched version of jmoby called 1.1.4-taverna which we host in our own repository [8]. Only the POM has been edited compared to jmoby 1.1.4 which was provided to us by Eddie Kawas from BioMoby. I don't know why he did not deploy this to [9] Also see below an email exchange with Ben Vandervalk who volunteered to bring our POM changes into the main jMoby codebase and do a 1.1.5 release. [1] http://www.mygrid.org.uk/taverna/updates/2.3.0/plugins/official/activities-2.3.0-20110905.xml [2] http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/biomoby-activity/pom.xml [3] http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/branches/maintenance/biomoby-activity/pom.xml [4] http://taverna.googlecode.com/svn/taverna/taverna-parent/trunk/pom.xml [5] http://taverna.googlecode.com/svn/taverna/taverna-parent/branches/maintenance/pom.xml [6] http://www.mygrid.org.uk/maven/biomoby/biomoby.org/m2repo/ [7] http://biomoby.org/m2repo [8] http://www.mygrid.org.uk/maven/repository/org/biomoby/jmoby/1.1.4-taverna/jmoby-1.1.4-taverna.pom [9] http://biomoby.org/m2repo/org/biomoby/jmoby/ On Fri, Aug 26, 2011 at 15:59, Stian Soiland-Reyes <[email protected]> wrote: > I believe JMoby 1.1.2, 1.1.3 and 1.1.4 was made specifically for > Taverna and probably not released as full Moby releases. Until 1.1.4 > there was not a single CVS tag for any of these. They didn't get > deployed properly as Eddie didn't have access to the Maven repository > server at the time. > > So the next version now would be 1.1.5 - most certainly not another 1.1.2! > > See attached email exchange with Eddie in the bottom of this message. > > > > Also note that we had to make our own POM file as the Moby team > refused our modifications upstream. So the -taverna versions in > http://www.mygrid.org.uk/maven/repository/org/biomoby/jmoby/ and > friends should be bytewise equal on the .jar as supplied by Moby, but > with modifications of the POM. > > I don't remember the reason for not accepting our patch, but I believe > it was due to some confusion about Maven warnings. I remember we had > to use a different axis declarations. I think I also had to remove a > dependency to really old Taverna jars in jmoby-desktop. > > Hopefully you would be able to pull in those POM changes for the 1.1.5 > release - you can just do a diff of the POM files from our repository > against what's in the CVS checkout. Feel free to ask me any questions, > and .. I'll try to remember or dig up the emails for why we did it a > certain way. Note that we no longer require Java 5 support, we use > Java 6 now. (I assume this update is for Taverna 2.3). > > > On Thu, Aug 25, 2011 at 14:34, Alan R Williams <[email protected]> wrote: >> Stian is looking up an e-mail exchange he had with Eddie when the current >> jar was created. >> >> Alan >> >> > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester > > > > > > > > ---------- Forwarded message ---------- > From: Stian Soiland-Reyes <[email protected]> > Date: Thu, Sep 2, 2010 at 11:24 > Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496 > To: Edward Kawas <[email protected]> > Cc: Mark Wilkinson <[email protected]> > > > We've already have two builds called 1.1.2 and 1.1.3 that I believe > you provided. I believe 1.1.3 was just a rebuild of 1.1.2, as 1.1.2 > was compiled for Java 6 instead of Java 5. > > I can't find any tags for any of these versions (and neither for > 1.1.1) in :pserver:[email protected]:/home/repository/moby - does > the code live somewhere else? > > This is all a bit messy - we need to know what version of jmoby to > include in Taverna, but it seems like jMoby basically isn't versioned. > > When you say that 'the bugs that are reported against BioMoby in > Taverna' are old bugs, which bugs do you mean? > > How can I verify that those bugs are fixed using the 1.1.1 JAR (or the > build you are talking about making - would that be 1.1.4 then? From > which code will it be built?). In which Taverna version did this work > as expected..? > > > Mark (cc): We're trying to clear up what JAR of jMoby is included in > Taverna 2.2.0, and which it should be, as Eddie suspects it is the > wrong one. > > > On Wed, Sep 1, 2010 at 15:14, Edward Kawas <[email protected]> wrote: >> I think that you are right about only having a customized pom. In any case, >> the jar that shipped with the latest Taverna is not the same as older >> versions (probably because of the version number mess; my fault). >> >> I think that if you could, you should try a newer version (I can build it >> for you) and we could label it version 1.1.2 and you could host it in the >> mygrid repository. I have never been able to access the Biomoby.org one. I >> had to always depend on someone else deploying it for me. >> >> The bugs that are reported regarding Biomoby in taverna 2.2.0 are old ones >> and were fixed some time ago. That's why we believe that an older version >> got thrown in by accident somehow. >> >> Eddie >> >> >>> -----Original Message----- >>> From: [email protected] [mailto:[email protected]] On Behalf Of Stian >>> Soiland-Reyes >>> Sent: Wednesday, September 01, 2010 7:05 AM >>> To: Edward Kawas >>> Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496 >>> >>> On Wed, Sep 1, 2010 at 14:52, Edward Kawas <[email protected]> >>> wrote: >>> > Hi Stian, >>> > >>> > The latest one that I know about is here: >>> http://biomoby.org/m2repo/org/biomoby/jmoby/1.1.1/ >>> > >>> > From what I remember, Taverna is using a custom version, hosted by you >>> (not personally, of course, but your project) somewhere. >>> >>> That matches >>> http://www.mygrid.org.uk/maven/repository/org/biomoby/jmoby/1.1.1- >>> taverna/ >>> >>> I don't think we have customized the JAR, just the POM. >>> >>> >>> >>> -- >>> Stian Soiland-Reyes, myGrid team >>> School of Computer Science >>> The University of Manchester >> >> > > > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester > > > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester > > > > > > > ---------- Forwarded message ---------- > From: Stian Soiland-Reyes <[email protected]> > Date: Fri, Sep 3, 2010 at 13:55 > Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496 > To: Edward Kawas <[email protected]> > Cc: Mark Wilkinson <[email protected]> > > > On Thu, Sep 2, 2010 at 19:28, Edward Kawas <[email protected]> wrote: >>> This is all a bit messy - we need to know what version of jmoby to include >>> in >>> Taverna, but it seems like jMoby basically isn't versioned. >> I thought that there were some version tags, but if you can't find them, I >> am obviously incorrect. > > I just had a quick look using Eclipse, tag discovery in CVS is > inherently tricky, so I won't claim you are incorrect :) > >>> When you say that 'the bugs that are reported against BioMoby in Taverna' >>> are old bugs, which bugs do you mean? >> The 'too many open' files bug. I believe that this was reported in version >> 1.7, but I can't find any reference to that > > No, I believe it was for 2.2.0. > >>> How can I verify that those bugs are fixed using the 1.1.1 JAR (or the build >>> you are talking about making - would that be 1.1.4 then? From which code >>> will it be built?). In which Taverna version did this work as expected..? >> The recent Biomoby errors in Taverna 2.2.0 won't occur on *nix machines. The >> library would be built from the latest Biomoby source. I may be wrong, but >> if you use an older version of Taverna, with the same jmoby version as is >> shipped with Taverna 2.2.0, the errors do not occur. > > So in Taverna 2.1.2 there is no problem, and the 'Moby Objects' folder > appear - even if the jMoby JAR there is byte-wise exactly the same? > > > Let's do a new build of jMoby, you call it 1.1.4 and make sure it's > tagged, and then I can add it to our repository with the updated POM. > We can then either wait till Taverna 2.3 (rougly scheduled end of > October) to release it, or do it as an online update, which should not > be too much work. > > I would suggest waiting until 2.3 if the current installation still > works, but just has an error-popup now and then, but if it is true > that the 'Moby Objects' folder is missing, we should do it as an > online update. > > > I'm unable to reproduce on my Ubuntu, but another colleague here has > also seen the pop-up now and then, so we can test your new JAR there. > > Just one thing - remember to compile it for Java 5, not java 6! (From > Taverna 2.3 Java 6-style should be OK, but not for a 2.2 update) > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester > > > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester > > > > > > ---------- Forwarded message ---------- > From: Edward Kawas <[email protected]> > Date: Thu, Sep 9, 2010 at 16:11 > Subject: RE: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496 > To: Stian Soiland-Reyes <[email protected]> > Cc: Mark Wilkinson <[email protected]> > > > Hi Stian, > > I added a tag to the moby cvs java/main branch and generated 2 jars > (target=1.5) for Taverna. I have attached them here. > > An immediate update would be best, because I think that running > Biomoby services is broken too when the error is encountered. > > Please let me know if I can be of further assistance. > > Thanks, > > Eddie > >> -----Original Message----- >> From: [email protected] [mailto:[email protected]] On Behalf Of Stian >> Soiland-Reyes >> Sent: Friday, September 03, 2010 5:56 AM >> To: Edward Kawas >> Cc: Mark Wilkinson >> Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496 >> >> On Thu, Sep 2, 2010 at 19:28, Edward Kawas <[email protected]> >> wrote: >> >> This is all a bit messy - we need to know what version of jmoby to >> >> include in Taverna, but it seems like jMoby basically isn't versioned. >> > I thought that there were some version tags, but if you can't find them, I >> am obviously incorrect. >> >> I just had a quick look using Eclipse, tag discovery in CVS is inherently >> tricky, >> so I won't claim you are incorrect :) >> >> >> When you say that 'the bugs that are reported against BioMoby in >> Taverna' >> >> are old bugs, which bugs do you mean? >> > The 'too many open' files bug. I believe that this was reported in >> > version 1.7, but I can't find any reference to that >> >> No, I believe it was for 2.2.0. >> >> >> How can I verify that those bugs are fixed using the 1.1.1 JAR (or >> >> the build you are talking about making - would that be 1.1.4 then? >> >> From which code will it be built?). In which Taverna version did this work >> as expected..? >> > The recent Biomoby errors in Taverna 2.2.0 won't occur on *nix machines. >> The library would be built from the latest Biomoby source. I may be wrong, >> but if you use an older version of Taverna, with the same jmoby version as is >> shipped with Taverna 2.2.0, the errors do not occur. >> >> So in Taverna 2.1.2 there is no problem, and the 'Moby Objects' folder >> appear - even if the jMoby JAR there is byte-wise exactly the same? >> >> >> Let's do a new build of jMoby, you call it 1.1.4 and make sure it's tagged, >> and >> then I can add it to our repository with the updated POM. >> We can then either wait till Taverna 2.3 (rougly scheduled end of >> October) to release it, or do it as an online update, which should not be too >> much work. >> >> I would suggest waiting until 2.3 if the current installation still works, >> but just >> has an error-popup now and then, but if it is true that the 'Moby Objects' >> folder is missing, we should do it as an online update. >> >> >> I'm unable to reproduce on my Ubuntu, but another colleague here has also >> seen the pop-up now and then, so we can test your new JAR there. >> >> Just one thing - remember to compile it for Java 5, not java 6! (From Taverna >> 2.3 Java 6-style should be OK, but not for a 2.2 update) >> >> -- >> Stian Soiland-Reyes, myGrid team >> School of Computer Science >> The University of Manchester > > > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester > -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. 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